TF reporter barcode processing - pMT02 - stimulation 3

Analysis

Based on these plots I will remove all samples that have less than 1,600 highly expressing barcodes, and all samples that have a correlation with the pDNA-bc counts of more than r=0.85

Normalization of barcode counts:

Divide cDNA barcode counts through pDNA barcode counts to get activity

Calculate mean activity - filter out outlier barcodes

Calculate correlations between technical replicates

Data quality plots - correlation between replicates

Session Info

paste("Run time: ",format(Sys.time()-StartTime))

## [1] "Run time:  3.815814 mins"

getwd()

## [1] "/DATA/usr/m.trauernicht/projects/SuRE-TF/gen-1_stimulation-3"

date()

## [1] "Wed Dec  9 10:59:27 2020"

sessionInfo()

## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.7 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/libblas/libblas.so.3.6.0
## LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] parallel  stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] gridExtra_2.3       RColorBrewer_1.1-2  readr_1.3.1        
##  [4] haven_2.2.0         ggbeeswarm_0.6.0    plotly_4.9.2.1     
##  [7] tibble_3.0.1        dplyr_0.8.5         vwr_0.3.0          
## [10] latticeExtra_0.6-29 lattice_0.20-38     stringdist_0.9.5.5 
## [13] GGally_1.5.0        ggpubr_0.2.5        magrittr_1.5       
## [16] ggplot2_3.3.0       stringr_1.4.0       plyr_1.8.6         
## [19] data.table_1.12.8  
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.5        tidyr_1.0.0       png_0.1-7         assertthat_0.2.1 
##  [5] digest_0.6.27     mime_0.9          R6_2.5.0          evaluate_0.14    
##  [9] httr_1.4.1        pillar_1.4.3      rlang_0.4.8       lazyeval_0.2.2   
## [13] Matrix_1.2-18     rmarkdown_2.5     splines_3.6.3     labeling_0.3     
## [17] htmlwidgets_1.5.2 munsell_0.5.0     shiny_1.4.0       compiler_3.6.3   
## [21] vipor_0.4.5       httpuv_1.5.4      xfun_0.19         pkgconfig_2.0.3  
## [25] mgcv_1.8-31       htmltools_0.5.0   tidyselect_1.1.0  reshape_0.8.8    
## [29] viridisLite_0.3.0 later_1.1.0.1     crayon_1.3.4      withr_2.1.2      
## [33] grid_3.6.3        nlme_3.1-143      xtable_1.8-4      jsonlite_1.7.1   
## [37] gtable_0.3.0      lifecycle_0.2.0   scales_1.1.0      stringi_1.5.3    
## [41] farver_2.0.1      ggsignif_0.6.0    reshape2_1.4.4    promises_1.1.1   
## [45] ellipsis_0.3.0    vctrs_0.2.4       tools_3.6.3       forcats_0.4.0    
## [49] glue_1.4.2        beeswarm_0.2.3    purrr_0.3.3       hms_0.5.3        
## [53] crosstalk_1.0.0   jpeg_0.1-8.1      prettydoc_0.4.0   fastmap_1.0.1    
## [57] yaml_2.2.1        colorspace_1.4-1  knitr_1.30